Generating an OHDSI OMOP Data Model from HCSRN's VDW

John Weeks

Introduction

  • OHDSI (pronounced “Odyssey”) OMOP
  • Why Generate OHDSI OMOP from your VDW
  • The VDW Data Translation Process
  • Implementing your Translation Scripts Locally

OHDSI (pronounced “Odyssey”) OMOP Common Data Model

  • What is the OHDSI OMOP Common Data Model?
    • A Common Data Model is a published data model that researchers can implement at their sites
    • Keeps their data secure
    • Allows them to share their code
      • Just like the VDW!
  • The Book of OHDSI is a great place to start learning about OHDSI OMOP.

Why Generate the OHDSI OMOP From Your VDW

Why is it important that the HCSRN sites be able to generate the OHDSI OMOP CDM?

  • Expanding Scientific Collaboration
  • Financial Support

Used in Projects Around the World

The OHDSI OMOP Common Data Model is used in collaborative healthcare research projects internationally.

Federal Grants Standardize Around the OHDSI OMOP

  • Precision Medicine Initiative: $130,000,000
  • 21st Century Cures Act: $1,800,000,000 over 7 years

VDW Data Translation Process

  • The Translation of Mapped Codes
  • The Translation of Data

Translating Codes

The OHDSI OMOP Vocabularies provide a sane approach to UMLS.

  • VDW standard codes are stored in the translation software
  • OHDSI OMOP standard codes are stored externally in the OHDSI Athena application

Data Translation Process

In broad terms most of the VDW entities have a corresponding OHDSI OMOP entity.

SAS Scripts to Translate Your Local VDW Into OMOP

Before you can translate your VDW into OHDSI OMOP you will need:

  • An implementation of the HCSRN VDW
  • Membership in OHDSI
  • The KPWHRI HCSRN-VDW to OHDSI OMOP SAS translation scripts
  • Download OHDSI OMOP CDM and Vocabulary Data

The HCSRN VDW Common Data Model

  • This SAS translation script requires an HCSRN Virtual Data Warehouse (VDW) data model at your site
  • Information about the VDW Common Data Model is available on the HCSRN website
  • HCSRN membership includes access to a large collection of SAS quality assurance scripts

Membership in OHDSI

Find information on how to become a member in The Book of OHDSI

  • Becoming a member of the OHDSI group will provide you access to a large collection of Open Source tools and data sets
  • Among those OHDSI tools you will find
    • OHDSI Atlas queries your OMOP common data model and saves cohort definitions
    • OHDSI Athena is an application that provides access to the OHDSI OMOP standard vocabularies

HCSRN-VDW-to-OHDSI-OMOP Translation Scripts

  • You can clone or download the scripts from VDW to OMOP GitHub webpage
  • These SAS scripts are published as Open Source software
  • They are freely available to anyone who is interested
  • The best of both worlds
  • Let's work together to expand these scripts to meet your needs

HCSRN VDW Code Sets

  • The SAS scripts include all of the standard codes and their descriptions that are unique to the HCSRN VDW.
  • During run time the scripts will generate a set of tables that map from the standard codes in your VDW to the OHDSI OMOP codes.

The HCSRN VDW Standard Codes include their descriptions, type and subject area source:

Code Code Description Code Type Code Source
F Female SEX_ADMIN DEMOGRAPHICS
GLU_F Blood Sugar Fasting TEST_TYPE LAB_RESULTS

The OHDSI OMOP Vocabulary Data

  • Download the OHDSI OMOP Vocabulary by going to the OHDSI Athena website
  • Extract the OHDSI OMOP Vocabulary CSV files into the "omop_vocab" folder

Final Thoughts

  • This project includes VDW standard codes and code management SAS scripts
  • This project is a work in progress AND you can be a part of that progress
  • Your feedback will help mature and harden the scripts for all of our users

Thank you for watching this presentation.

my email address is: John.M.Weeks@kp.org

List of URLs Referenced in Presentation